Mutagenetix > Incidental Mutation

Incidental Mutation 'R0047:Mtr'

32989

Institutional Source

Beutler Lab

Gene Symbol

Mtr

Ensembl Gene

ENSMUSG00000021311

Gene Name

5-methyltetrahydrofolate-homocysteine methyltransferase

Synonyms

methionine synthase, D830038K18Rik, MS

MMRRC Submission

038341-MU

Accession Numbers

Genbank: NM_001081128

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0047 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

12182712-12258113 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 12222226 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 569 (S569T)

Ref Sequence

ENSEMBL: ENSMUSP00000097442 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000099856] [ENSMUST00000221290]

AlphaFold

A6H5Y3

Predicted Effect

probably damaging
Transcript: ENSMUST00000099856
AA Change: S569T

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000097442
Gene: ENSMUSG00000021311
AA Change: S569T

Domain	Start	End	E-Value	Type
Pfam:S-methyl_trans	18	326	1.5e-93	PFAM
Pfam:Pterin_bind	363	601	4.6e-63	PFAM
B12-binding_2	657	743	6.42e-41	SMART
Pfam:B12-binding	761	861	3.3e-20	PFAM
Pfam:Met_synt_B12	953	1234	2.5e-114	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000221290

Meta Mutation Damage Score

0.6960

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.0%
20x: 94.8%

Validation Efficiency

100% (98/98)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]
PHENOTYPE: Mice homozygous for a targeted null mutation exhibit embryonic lethality prior to E9.5. Heterozygous appear mostly similar to conrtols, except that they exhibit elevated plasma methionine and homocysteine levels. [provided by MGI curators]

Allele List at MGI

All alleles(6) : Targeted, knock-out(1) Gene trapped(5)

Other mutations in this stock

Total: 99 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 138,066,264	T405A	probably damaging	Het
4932438A13Rik	T	A	3: 36,908,192	L481M	possibly damaging	Het
Acer1	A	T	17: 56,955,624	D175E	possibly damaging	Het
Acsf2	T	C	11: 94,569,342	I395V	probably benign	Het
Adamts9	G	A	6: 92,905,306		probably benign	Het
Amigo3	T	C	9: 108,054,658	S427P	probably benign	Het
Ankrd35	A	G	3: 96,684,063	K555R	probably benign	Het
Arhgap35	A	T	7: 16,561,992	H1049Q	probably benign	Het
Arhgef5	G	A	6: 43,265,621		probably null	Het
Arid4a	T	G	12: 71,075,419	L858W	probably damaging	Het
Bbox1	A	G	2: 110,268,302	F310S	probably damaging	Het
Bhlhe22	T	C	3: 18,055,569	L261P	probably damaging	Het
Bmper	T	A	9: 23,406,686	C534S	probably damaging	Het
Cacna1d	T	G	14: 30,346,790		probably benign	Het
Camk2g	G	A	14: 20,771,068		probably benign	Het
Capn12	G	A	7: 28,890,387		probably null	Het
Cdkl4	T	G	17: 80,550,845	N115T	probably benign	Het
Chchd1	T	C	14: 20,704,163	S48P	possibly damaging	Het
Chia1	G	T	3: 106,115,257	C49F	probably damaging	Het
Cnot7	A	G	8: 40,495,921		probably benign	Het
Crh	T	C	3: 19,694,037	E147G	probably damaging	Het
Cux1	T	C	5: 136,363,253		probably benign	Het
Cyp2b19	T	A	7: 26,766,826	D351E	probably benign	Het
Dctn1	G	T	6: 83,182,632	G31*	probably null	Het
Duox1	T	A	2: 122,346,641		probably benign	Het
Egflam	T	G	15: 7,253,430	E382A	possibly damaging	Het
Ext1	T	C	15: 53,345,146	N73S	probably benign	Het
Ffar4	A	G	19: 38,114,004		probably benign	Het
Glg1	A	T	8: 111,165,582	M866K	probably damaging	Het
Golm1	T	A	13: 59,645,100	H197L	probably benign	Het
Gtse1	A	G	15: 85,862,378	K132E	probably damaging	Het
Gxylt2	A	T	6: 100,733,378		probably benign	Het
Hrc	T	A	7: 45,336,689	S421R	probably benign	Het
Ighg2c	T	A	12: 113,288,168		probably benign	Het
Ihh	A	G	1: 74,946,591	I245T	probably benign	Het
Ilf3	T	A	9: 21,388,714	M65K	possibly damaging	Het
Insr	A	G	8: 3,202,947	V404A	probably damaging	Het
Irak2	G	T	6: 113,672,953		probably benign	Het
Irak2	G	A	6: 113,678,738	V367I	probably benign	Het
Kat7	A	C	11: 95,300,208	N119K	probably benign	Het
Kif9	A	G	9: 110,485,038	I33V	probably benign	Het
Klf17	A	G	4: 117,761,032	Y43H	probably benign	Het
Kng2	T	A	16: 22,987,563	T629S	possibly damaging	Het
Lama1	A	T	17: 67,795,186		probably benign	Het
Lamb1	T	C	12: 31,278,601	I188T	possibly damaging	Het
Lpp	T	A	16: 24,661,800		probably benign	Het
Lrp12	T	C	15: 39,878,239	E360G	probably damaging	Het
Mark2	A	C	19: 7,283,577		probably benign	Het
Mmp3	T	C	9: 7,451,910		probably benign	Het
Mthfd1l	T	A	10: 3,978,727		probably benign	Het
Myh13	T	A	11: 67,367,237	S1752T	probably benign	Het
Myo5a	T	A	9: 75,156,207	L565H	probably damaging	Het
Nanos3	C	T	8: 84,176,134	R133Q	probably damaging	Het
Nfkb1	A	T	3: 135,595,053	L72*	probably null	Het
Numa1	A	G	7: 102,009,453	K296E	probably damaging	Het
Olfr1477	A	G	19: 13,502,589	E82G	probably benign	Het
Olfr186	T	A	16: 59,027,224	M228L	probably benign	Het
Olfr201	C	T	16: 59,269,211	G152D	probably damaging	Het
Olfr508	A	G	7: 108,630,552	I187V	probably benign	Het
Olfr613	A	T	7: 103,552,322	Y179F	probably damaging	Het
Pcdhb5	A	T	18: 37,321,268	I234F	possibly damaging	Het
Pgm5	T	A	19: 24,684,556	I545F	probably damaging	Het
Pla2g2c	T	C	4: 138,743,590		probably benign	Het
Pnpla7	A	T	2: 25,011,606	E548V	probably damaging	Het
Ppm1m	C	A	9: 106,196,696	E273*	probably null	Het
Ppp2r1b	C	T	9: 50,861,573	R117*	probably null	Het
Rabgap1l	G	A	1: 160,231,789		probably benign	Het
Rapgef6	T	A	11: 54,546,378	M49K	possibly damaging	Het
Rhox4f	A	C	X: 37,607,469	V15G	probably benign	Het
Rnf219	T	A	14: 104,503,344		probably null	Het
Rtel1	T	G	2: 181,323,405	I146M	probably damaging	Het
Sdr9c7	A	T	10: 127,903,672	M219L	probably benign	Het
Serpina3g	T	A	12: 104,240,284	S115T	possibly damaging	Het
Serpinb1a	A	T	13: 32,850,276	L44Q	probably damaging	Het
Slc13a4	A	G	6: 35,287,362	I190T	possibly damaging	Het
Slc46a2	A	G	4: 59,914,392	L177P	probably damaging	Het
Slc47a2	C	T	11: 61,336,242	V167M	possibly damaging	Het
Snrnp200	C	T	2: 127,234,954		probably benign	Het
Snx13	C	A	12: 35,101,124		probably benign	Het
Snx25	C	T	8: 46,041,365	A828T	probably damaging	Het
Spic	A	G	10: 88,675,941	L151P	probably damaging	Het
Ssu2	G	A	6: 112,374,820	H315Y	probably damaging	Het
Stk32a	T	C	18: 43,313,378		probably benign	Het
Tbx3	A	T	5: 119,680,446	E382V	probably damaging	Het
Tcaf2	A	G	6: 42,629,613	I469T	probably benign	Het
Tln2	A	G	9: 67,240,672		probably benign	Het
Top2a	T	A	11: 98,997,856	I1260L	probably benign	Het
Treml1	C	A	17: 48,364,980	S91*	probably null	Het
Trim26	T	C	17: 36,857,864		probably benign	Het
Trmt11	T	C	10: 30,535,243	N418S	probably benign	Het
Ttf1	A	G	2: 29,084,655	Y801C	probably damaging	Het
Usp34	C	T	11: 23,464,403	A2782V	probably benign	Het
Vmn2r77	T	C	7: 86,811,650	V728A	probably benign	Het
Vps4a	T	C	8: 107,036,701	L29P	probably damaging	Het
Wdfy3	A	G	5: 101,944,033	I480T	probably damaging	Het
Wdr41	A	G	13: 95,010,287	I197V	probably damaging	Het
Ywhag	A	T	5: 135,911,299	V147E	probably damaging	Het
Zan	A	G	5: 137,403,656	M4058T	unknown	Het
Zfp236	C	T	18: 82,680,692	C88Y	probably damaging	Het

Other mutations in Mtr

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01299:Mtr	APN	13	12225650	splice site	probably benign
IGL02456:Mtr	APN	13	12199094	missense	probably damaging	0.98
IGL02573:Mtr	APN	13	12199127	missense	possibly damaging	0.95
IGL02642:Mtr	APN	13	12195232	splice site	probably benign
IGL03005:Mtr	APN	13	12235449	splice site	probably benign
IGL03017:Mtr	APN	13	12247891	critical splice donor site	probably null
IGL03036:Mtr	APN	13	12247377	missense	probably damaging	1.00
H8930:Mtr	UTSW	13	12235460	missense	probably damaging	1.00
PIT4431001:Mtr	UTSW	13	12212443	missense	probably damaging	1.00
PIT4520001:Mtr	UTSW	13	12197985	nonsense	probably null
R0011:Mtr	UTSW	13	12238052	splice site	probably benign
R0047:Mtr	UTSW	13	12222226	missense	probably damaging	1.00
R0304:Mtr	UTSW	13	12222154	critical splice donor site	probably null
R0617:Mtr	UTSW	13	12221432	missense	probably benign
R0842:Mtr	UTSW	13	12200247	missense	probably damaging	1.00
R1101:Mtr	UTSW	13	12189525	missense	possibly damaging	0.84
R1450:Mtr	UTSW	13	12193733	missense	probably damaging	0.99
R1534:Mtr	UTSW	13	12235544	splice site	probably benign
R1907:Mtr	UTSW	13	12225532	missense	probably damaging	1.00
R2111:Mtr	UTSW	13	12244601	missense	possibly damaging	0.86
R2354:Mtr	UTSW	13	12188157	splice site	probably benign
R3849:Mtr	UTSW	13	12247365	missense	probably benign	0.16
R3899:Mtr	UTSW	13	12216849	missense	probably benign	0.00
R4012:Mtr	UTSW	13	12189397	missense	probably damaging	1.00
R4012:Mtr	UTSW	13	12189398	missense	probably damaging	1.00
R4075:Mtr	UTSW	13	12215412	critical splice donor site	probably null
R4091:Mtr	UTSW	13	12231057	missense	probably damaging	1.00
R4655:Mtr	UTSW	13	12227793	missense	probably damaging	1.00
R4801:Mtr	UTSW	13	12195251	missense	probably benign	0.01
R4802:Mtr	UTSW	13	12195251	missense	probably benign	0.01
R4895:Mtr	UTSW	13	12216866	missense	probably benign	0.01
R5481:Mtr	UTSW	13	12188155	critical splice acceptor site	probably null
R5966:Mtr	UTSW	13	12215567	critical splice acceptor site	probably null
R6209:Mtr	UTSW	13	12190392	missense	probably benign	0.00
R6348:Mtr	UTSW	13	12247954	missense	possibly damaging	0.49
R6463:Mtr	UTSW	13	12216866	missense	probably benign	0.01
R6467:Mtr	UTSW	13	12188106	missense	probably damaging	1.00
R7046:Mtr	UTSW	13	12190209	missense	possibly damaging	0.58
R7505:Mtr	UTSW	13	12221476	missense	probably benign	0.02
R7575:Mtr	UTSW	13	12199077	missense	probably benign	0.01
R7705:Mtr	UTSW	13	12249896	missense	probably benign
R7748:Mtr	UTSW	13	12227839	missense	probably benign	0.00
R8161:Mtr	UTSW	13	12221486	missense	probably damaging	0.99
R8290:Mtr	UTSW	13	12190253	missense	probably damaging	1.00
R8988:Mtr	UTSW	13	12235479	missense	probably benign
R9050:Mtr	UTSW	13	12216862	missense	probably null	0.67
R9420:Mtr	UTSW	13	12253878	missense	probably benign	0.04
R9655:Mtr	UTSW	13	12188144	missense	probably damaging	1.00
X0064:Mtr	UTSW	13	12250657	missense	probably damaging	1.00
Z1177:Mtr	UTSW	13	12187049	missense	probably benign	0.32
Z1177:Mtr	UTSW	13	12249866	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GAGCAGTCCAGTTATCCGCAGAAC -3'
(R):5'- ACATGGCACTGTAATGTGGCAGAC -3'

Sequencing Primer
(F):5'- tctcttgtttgccactgacc -3'
(R):5'- GGCTTTGTCTAGTAACAAGTTCAG -3'

Posted On

2013-05-09